Here’s a shot in the dark for you.
When working on my Mac in files on iCloud Drive (and indexed into DEVONthink), sometimes the files get duplicated.
I can discern no pattern to this. Sometime soon I’ll break out the scientific method to figure it out, but it’s so inconsistent that even gathering data on different scenarios will be extremely tedious. My suspicion is that it’s something to do with iCloud, because this didn’t previously happen on Dropbox.
It’s not really a problem. I just delete the copies and move on. Still, if someone else has experienced this and resolved it before, I’d love to know what’s going on.